Contacts of the strand formed by residues 155 - 160 (chain B) in PDB entry 1M1B
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B THR 4.1 0.9 - - - -
11B LEU* 4.0 15.0 - - + -
12B LYS* 3.4 42.8 - - - -
15B LEU* 3.8 24.9 - - + -
83B LEU* 4.8 1.3 - - + +
109B ALA 3.2 6.1 + - - -
110B GLY* 3.0 5.4 - - - -
111B ALA 2.9 25.6 + - - +
153B ASP 3.2 15.9 - - - -
154B PHE* 1.3 73.6 - - - +
156B ILE* 1.3 62.5 + - - +
157B VAL* 3.8 1.7 + - + -
185B ASP* 3.4 9.4 - - + +
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 4.0 15.7 - - + -
111B ALA* 3.4 14.1 - - + +
113B LEU* 4.6 5.4 - - + -
142B ILE* 4.0 37.7 - - + -
145B CYS* 3.7 30.1 - - + -
146B LYS* 3.7 25.6 - - + -
149B GLN* 3.9 9.2 - - - +
154B PHE* 4.0 16.8 + - + -
155B CYS* 1.3 72.7 - - - +
157B VAL* 1.3 63.7 + - - +
184B ALA* 3.6 2.3 - - - -
185B ASP* 2.7 36.9 + - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 3.9 30.1 - - + -
83B LEU* 4.0 24.5 - - + -
111B ALA 2.7 9.2 + - - +
112B CYS* 2.9 22.4 - - + -
113B LEU 2.8 30.3 + - - -
155B CYS* 4.9 2.0 - - + -
156B ILE* 1.3 79.1 - - - +
158B ALA* 1.3 63.4 + - - +
186B ALA* 3.6 23.8 - - + +
187B ILE 4.6 0.2 - - - -
188B LEU* 4.1 20.6 - - + +
213B VAL* 4.7 5.2 - - + -
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU 3.7 3.8 - - - -
138B PHE* 4.4 0.9 - - + -
142B ILE* 4.0 17.7 - - + -
156B ILE 3.8 1.8 + - - -
157B VAL* 1.3 71.9 - - - +
159B ARG* 1.3 58.8 + - - +
160B VAL 4.1 0.7 + - - -
179B TYR* 3.7 35.0 - - + -
184B ALA* 3.7 16.4 - - + -
186B ALA 3.0 7.2 + - - +
187B ILE* 3.3 9.2 - - + +
188B LEU 2.8 24.6 + - - +
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TRP* 4.1 10.1 - - - -
85B ASP* 3.6 16.4 + - - -
112B CYS* 3.5 22.0 - - - -
113B LEU 2.7 17.2 + - - +
114B GLU* 3.3 26.9 + - + +
115B ASP* 2.8 29.3 + - - +
116B LYS* 5.3 0.2 - - - +
120B LYS* 5.6 0.4 - - - +
123B SER* 3.7 5.5 + - - -
138B PHE* 4.7 2.0 - - - -
157B VAL 3.9 0.2 + - - -
158B ALA* 1.3 73.8 - - - +
160B VAL* 1.3 64.8 + - - +
161B GLU* 3.0 26.4 + - - +
179B TYR* 5.0 1.3 - - - -
188B LEU* 3.4 25.5 - - + +
190B HIS* 3.8 15.7 - - + +
215B VAL* 6.2 1.5 - - - +
997B SPV 2.9 48.6 + - - +
999B MG 3.8 2.2 - - - -
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASP* 3.6 4.5 - - - +
158B ALA 4.9 0.2 - - - +
159B ARG* 1.3 73.8 - - - +
161B GLU* 1.3 62.3 + - - +
162B ALA* 3.7 24.0 - - + +
163B PHE 5.2 0.2 + - - -
172B ALA* 4.0 9.4 - - - +
175B ARG* 4.3 7.4 - - + -
176B ALA* 3.9 30.1 - - + +
179B TYR* 4.1 13.7 - - + -
187B ILE* 4.0 15.9 - - + -
188B LEU 2.8 12.3 + - - +
189B MET* 3.9 23.8 - - + +
190B HIS* 3.4 27.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il